physiologies imports a list of data.frames. This data is in "raw"
state before cleaning and going through the data imputation steps. It
should be used by developers/curators of the package.
physiologies(keyword = "all", fullSource = FALSE)Character vector with one or more valid keywords.
Valid keyboards can be checked with showPhys. If 'all', all
physiologies are imported.
Logical. If TRUE, the Attribute_source column will
contain full source information. If FALSE, the Attribute_source column
will contain shortened versions of the sources. Default is FALSE.
A list of data.frames in tidy format.
l <- physiologies('all')
#> All physiologies will be imported.
#> Finished COGEM pathogenicity rating.
#> Finished acetate producing.
#> Finished aerophilicity.
#> Finished animal pathogen.
#> Finished antimicrobial resistance.
#> Finished antimicrobial sensitivity.
#> Finished arrangement.
#> Finished biofilm formation.
#> Finished biosafety level.
#> Finished butyrate producing.
#> Finished coding genes.
#> Finished country.
#> Finished disease association.
#> Finished extreme environment.
#> Finished genome size.
#> Finished geographic location.
#> Finished gram stain.
#> Finished growth medium.
#> Finished growth temperature.
#> Finished habitat.
#> Finished halophily.
#> Finished health associated.
#> Finished hemolysis.
#> Finished host-associated.
#> Finished hydrogen gas producing.
#> Finished isolation site.
#> Finished lactate producing.
#> Finished length.
#> Finished metabolite production.
#> Finished metabolite utilization.
#> Finished motility.
#> Finished mutation rate per site per generation.
#> Finished mutation rate per site per year.
#> Finished optimal ph.
#> Finished pathogenicity human.
#> Finished plant pathogenicity.
#> Finished shape.
#> Finished sphingolipid producing.
#> Finished spore formation.
#> Finished spore shape.
#> Finished width.
#> Warning: Missing columns in halophily. Missing columns are: Genome_ID, Accession_ID
df <- physiologies('aerophilicity')[[1]]
#> Finished aerophilicity.